Examples with SimulationSymbolTable cbit.vcell.solver.SimulationSymbolTable used on opensource projects

Example 6 with SimulationSymbolTable

use of cbit.vcell.solver.SimulationSymbolTable in project vcell by virtualcell.

the class DefaultODESolver method createODESolverResultSet.

/**
 */
private ODESolverResultSet createODESolverResultSet() throws ExpressionException {
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    // 
    // create symbol table for binding expression
    // 
    String[] symbols = new String[fieldIdentifiers.size()];
    for (int i = 0; i < symbols.length; i++) {
        symbols[i] = ((Variable) fieldIdentifiers.elementAt(i)).getName();
    }
    // Initialize the ResultSet...
    ODESolverResultSet odeSolverResultSet = new ODESolverResultSet();
    odeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(ReservedVariable.TIME.getName()));
    for (int i = 0; i < getStateVariableCount(); i++) {
        StateVariable stateVariable = getStateVariable(i);
        if (stateVariable instanceof SensStateVariable) {
            SensStateVariable sensStateVariable = (SensStateVariable) stateVariable;
            odeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(sensStateVariable.getVariable().getName(), sensStateVariable.getParameter().getName(), sensStateVariable.getVariable().getName()));
        } else {
            odeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(stateVariable.getVariable().getName()));
        }
    }
    Variable[] variables = simSymbolTable.getVariables();
    for (int i = 0; i < variables.length; i++) {
        if (variables[i] instanceof Function && SimulationSymbolTable.isFunctionSaved((Function) variables[i])) {
            Function function = (Function) variables[i];
            Expression exp1 = new Expression(function.getExpression());
            try {
                exp1 = simSymbolTable.substituteFunctions(exp1);
            } catch (MathException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException("Substitute function failed on function " + function.getName() + " " + e.getMessage());
            }
            odeSolverResultSet.addFunctionColumn(new FunctionColumnDescription(exp1.flatten(), function.getName(), null, function.getName(), false));
        }
    }
    // 
    if (getSensitivityParameter() != null) {
        if (odeSolverResultSet.findColumn(getSensitivityParameter().getName()) == -1) {
            FunctionColumnDescription fcd = new FunctionColumnDescription(new Expression(getSensitivityParameter().getConstantValue()), getSensitivityParameter().getName(), null, getSensitivityParameter().getName(), false);
            odeSolverResultSet.addFunctionColumn(fcd);
        }
        StateVariable[] stateVars = (StateVariable[]) org.vcell.util.BeanUtils.getArray(fieldStateVariables, StateVariable.class);
        for (int i = 0; i < variables.length; i++) {
            if (variables[i] instanceof Function && SimulationSymbolTable.isFunctionSaved((Function) variables[i])) {
                Function depSensFunction = (Function) variables[i];
                Expression depSensFnExpr = new Expression(depSensFunction.getExpression());
                try {
                    depSensFnExpr = simSymbolTable.substituteFunctions(depSensFnExpr);
                } catch (MathException e) {
                    e.printStackTrace(System.out);
                    throw new RuntimeException("Substitute function failed on function " + depSensFunction.getName() + " " + e.getMessage());
                }
                depSensFnExpr = getFunctionSensitivity(depSensFnExpr, getSensitivityParameter(), stateVars);
                // depSensFnExpr = depSensFnExpr.flatten(); 	// already bound and flattened in getFunctionSensitivity, no need here ...
                String depSensFnName = new String("sens_" + depSensFunction.getName() + "_wrt_" + getSensitivityParameter().getName());
                if (depSensFunction != null) {
                    FunctionColumnDescription cd = new FunctionColumnDescription(depSensFnExpr.flatten(), depSensFnName, getSensitivityParameter().getName(), depSensFnName, false);
                    odeSolverResultSet.addFunctionColumn(cd);
                }
            }
        }
    }
    return (odeSolverResultSet);
}

Example 7 with SimulationSymbolTable

use of cbit.vcell.solver.SimulationSymbolTable in project vcell by virtualcell.

the class IDAFileWriter method writeEquations.

/**
 * Insert the method's description here.
 * Creation date: (3/8/00 10:31:52 PM)
 */
protected String writeEquations(HashMap<Discontinuity, String> discontinuityNameMap) throws MathException, ExpressionException {
    Simulation simulation = simTask.getSimulation();
    StringBuffer sb = new StringBuffer();
    MathDescription mathDescription = simulation.getMathDescription();
    if (mathDescription.hasFastSystems()) {
        // 
        // define vector of original variables
        // 
        SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
        CompartmentSubDomain subDomain = (CompartmentSubDomain) mathDescription.getSubDomains().nextElement();
        FastSystem fastSystem = subDomain.getFastSystem();
        FastSystemAnalyzer fs_Analyzer = new FastSystemAnalyzer(fastSystem, simSymbolTable);
        int numIndependent = fs_Analyzer.getNumIndependentVariables();
        int systemDim = mathDescription.getStateVariableNames().size();
        int numDependent = systemDim - numIndependent;
        // 
        // get all variables from fast system (dependent and independent)
        // 
        HashSet<String> fastSystemVarHash = new HashSet<String>();
        Enumeration<Variable> dependentfastSystemVarEnum = fs_Analyzer.getDependentVariables();
        while (dependentfastSystemVarEnum.hasMoreElements()) {
            fastSystemVarHash.add(dependentfastSystemVarEnum.nextElement().getName());
        }
        Enumeration<Variable> independentfastSystemVarEnum = fs_Analyzer.getIndependentVariables();
        while (independentfastSystemVarEnum.hasMoreElements()) {
            fastSystemVarHash.add(independentfastSystemVarEnum.nextElement().getName());
        }
        // 
        // get all equations including for variables that are not in the fastSystem (ode equations for "slow system")
        // 
        RationalExpMatrix origInitVector = new RationalExpMatrix(systemDim, 1);
        RationalExpMatrix origSlowRateVector = new RationalExpMatrix(systemDim, 1);
        RationalExpMatrix origVarColumnVector = new RationalExpMatrix(systemDim, 1);
        Enumeration<Equation> enumEquations = subDomain.getEquations();
        int varIndex = 0;
        while (enumEquations.hasMoreElements()) {
            Equation equation = enumEquations.nextElement();
            origVarColumnVector.set_elem(varIndex, 0, new RationalExp(equation.getVariable().getName()));
            Expression rateExpr = equation.getRateExpression();
            rateExpr.bindExpression(varsSymbolTable);
            rateExpr = MathUtilities.substituteFunctions(rateExpr, varsSymbolTable);
            origSlowRateVector.set_elem(varIndex, 0, new RationalExp("(" + rateExpr.flatten().infix() + ")"));
            Expression initExpr = new Expression(equation.getInitialExpression());
            initExpr.substituteInPlace(new Expression("t"), new Expression(0.0));
            initExpr = MathUtilities.substituteFunctions(initExpr, varsSymbolTable).flatten();
            origInitVector.set_elem(varIndex, 0, new RationalExp("(" + initExpr.flatten().infix() + ")"));
            varIndex++;
        }
        // 
        // make symbolic matrix for fast invariants (from FastSystem's fastInvariants as well as a new fast invariant for each variable not included in the fast system.
        // 
        RationalExpMatrix fastInvarianceMatrix = new RationalExpMatrix(numDependent, systemDim);
        int row = 0;
        for (int i = 0; i < origVarColumnVector.getNumRows(); i++) {
            // 
            if (!fastSystemVarHash.contains(origVarColumnVector.get(i, 0).infixString())) {
                fastInvarianceMatrix.set_elem(row, i, RationalExp.ONE);
                row++;
            }
        }
        Enumeration<FastInvariant> enumFastInvariants = fastSystem.getFastInvariants();
        while (enumFastInvariants.hasMoreElements()) {
            FastInvariant fastInvariant = enumFastInvariants.nextElement();
            Expression fastInvariantExpression = fastInvariant.getFunction();
            for (int col = 0; col < systemDim; col++) {
                Expression coeff = fastInvariantExpression.differentiate(origVarColumnVector.get(col, 0).infixString()).flatten();
                coeff = simSymbolTable.substituteFunctions(coeff);
                fastInvarianceMatrix.set_elem(row, col, RationalExpUtils.getRationalExp(coeff));
            }
            row++;
        }
        for (int i = 0; i < systemDim; i++) {
            sb.append("VAR " + origVarColumnVector.get(i, 0).infixString() + " INIT " + origInitVector.get(i, 0).infixString() + ";\n");
        }
        RationalExpMatrix fullMatrix = null;
        RationalExpMatrix inverseFullMatrix = null;
        RationalExpMatrix newSlowRateVector = null;
        try {
            RationalExpMatrix fastMat = ((RationalExpMatrix) fastInvarianceMatrix.transpose().findNullSpace());
            fullMatrix = new RationalExpMatrix(systemDim, systemDim);
            row = 0;
            for (int i = 0; i < fastInvarianceMatrix.getNumRows(); i++) {
                for (int col = 0; col < systemDim; col++) {
                    fullMatrix.set_elem(row, col, fastInvarianceMatrix.get(i, col));
                }
                row++;
            }
            for (int i = 0; i < fastMat.getNumRows(); i++) {
                for (int col = 0; col < systemDim; col++) {
                    fullMatrix.set_elem(row, col, fastMat.get(i, col));
                }
                row++;
            }
            inverseFullMatrix = new RationalExpMatrix(systemDim, systemDim);
            inverseFullMatrix.identity();
            RationalExpMatrix copyOfFullMatrix = new RationalExpMatrix(fullMatrix);
            copyOfFullMatrix.gaussianElimination(inverseFullMatrix);
            newSlowRateVector = new RationalExpMatrix(numDependent, 1);
            newSlowRateVector.matmul(fastInvarianceMatrix, origSlowRateVector);
        } catch (MatrixException ex) {
            ex.printStackTrace();
            throw new MathException(ex.getMessage());
        }
        sb.append("TRANSFORM\n");
        for (row = 0; row < systemDim; row++) {
            for (int col = 0; col < systemDim; col++) {
                sb.append(fullMatrix.get(row, col).getConstant().doubleValue() + " ");
            }
            sb.append("\n");
        }
        sb.append("INVERSETRANSFORM\n");
        for (row = 0; row < systemDim; row++) {
            for (int col = 0; col < systemDim; col++) {
                sb.append(inverseFullMatrix.get(row, col).getConstant().doubleValue() + " ");
            }
            sb.append("\n");
        }
        int numDifferential = numDependent;
        int numAlgebraic = numIndependent;
        sb.append("RHS DIFFERENTIAL " + numDifferential + " ALGEBRAIC " + numAlgebraic + "\n");
        int equationIndex = 0;
        while (equationIndex < numDependent) {
            // print row of mass matrix followed by slow rate corresponding to fast invariant
            Expression slowRateExp = new Expression(newSlowRateVector.get(equationIndex, 0).infixString()).flatten();
            slowRateExp.bindExpression(simSymbolTable);
            slowRateExp = MathUtilities.substituteFunctions(slowRateExp, varsSymbolTable).flatten();
            Vector<Discontinuity> v = slowRateExp.getDiscontinuities();
            for (Discontinuity od : v) {
                od = getSubsitutedAndFlattened(od, varsSymbolTable);
                String dname = discontinuityNameMap.get(od);
                if (dname == null) {
                    dname = ROOT_VARIABLE_PREFIX + discontinuityNameMap.size();
                    discontinuityNameMap.put(od, dname);
                }
                slowRateExp.substituteInPlace(od.getDiscontinuityExp(), new Expression("(" + dname + "==1)"));
            }
            sb.append(slowRateExp.infix() + ";\n");
            equationIndex++;
        }
        Enumeration<FastRate> enumFastRates = fastSystem.getFastRates();
        while (enumFastRates.hasMoreElements()) {
            // print the fastRate for this row
            Expression fastRateExp = new Expression(enumFastRates.nextElement().getFunction());
            fastRateExp = MathUtilities.substituteFunctions(fastRateExp, varsSymbolTable).flatten();
            Vector<Discontinuity> v = fastRateExp.getDiscontinuities();
            for (Discontinuity od : v) {
                od = getSubsitutedAndFlattened(od, varsSymbolTable);
                String dname = discontinuityNameMap.get(od);
                if (dname == null) {
                    dname = ROOT_VARIABLE_PREFIX + discontinuityNameMap.size();
                    discontinuityNameMap.put(od, dname);
                }
                fastRateExp.substituteInPlace(od.getDiscontinuityExp(), new Expression("(" + dname + "==1)"));
            }
            sb.append(fastRateExp.flatten().infix() + ";\n");
            equationIndex++;
        }
    } else {
        for (int i = 0; i < getStateVariableCount(); i++) {
            StateVariable stateVar = getStateVariable(i);
            Expression initExpr = new Expression(stateVar.getInitialRateExpression());
            initExpr = MathUtilities.substituteFunctions(initExpr, varsSymbolTable);
            initExpr.substituteInPlace(new Expression("t"), new Expression(0.0));
            sb.append("VAR " + stateVar.getVariable().getName() + " INIT " + initExpr.flatten().infix() + ";\n");
        }
        sb.append("TRANSFORM\n");
        for (int row = 0; row < getStateVariableCount(); row++) {
            for (int col = 0; col < getStateVariableCount(); col++) {
                sb.append((row == col ? 1 : 0) + " ");
            }
            sb.append("\n");
        }
        sb.append("INVERSETRANSFORM\n");
        for (int row = 0; row < getStateVariableCount(); row++) {
            for (int col = 0; col < getStateVariableCount(); col++) {
                sb.append((row == col ? 1 : 0) + " ");
            }
            sb.append("\n");
        }
        sb.append("RHS DIFFERENTIAL " + getStateVariableCount() + " ALGEBRAIC 0\n");
        for (int i = 0; i < getStateVariableCount(); i++) {
            StateVariable stateVar = getStateVariable(i);
            Expression rateExpr = new Expression(stateVar.getRateExpression());
            rateExpr = MathUtilities.substituteFunctions(rateExpr, varsSymbolTable).flatten();
            Vector<Discontinuity> v = rateExpr.getDiscontinuities();
            for (Discontinuity od : v) {
                od = getSubsitutedAndFlattened(od, varsSymbolTable);
                String dname = discontinuityNameMap.get(od);
                if (dname == null) {
                    dname = ROOT_VARIABLE_PREFIX + discontinuityNameMap.size();
                    discontinuityNameMap.put(od, dname);
                }
                rateExpr.substituteInPlace(od.getDiscontinuityExp(), new Expression("(" + dname + "==1)"));
            }
            sb.append(rateExpr.infix() + ";\n");
        }
    }
    return sb.toString();
}

Example 8 with SimulationSymbolTable

use of cbit.vcell.solver.SimulationSymbolTable in project vcell by virtualcell.

the class SundialsSolver method getODESolverResultSet.

/**
 * This method was created in VisualAge.
 * @return double[]
 * @param vectorIndex int
 */
public ODESolverResultSet getODESolverResultSet() {
    // 
    // read .ida file
    // 
    ODESolverResultSet odeSolverResultSet = getStateVariableResultSet();
    if (odeSolverResultSet == null) {
        return null;
    }
    // 
    // add appropriate Function columns to result set
    // 
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    Function[] functions = simSymbolTable.getFunctions();
    for (int i = 0; i < functions.length; i++) {
        if (SimulationSymbolTable.isFunctionSaved(functions[i])) {
            Expression exp1 = new Expression(functions[i].getExpression());
            try {
                exp1 = simSymbolTable.substituteFunctions(exp1);
            } catch (MathException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException("Substitute function failed on function " + functions[i].getName() + " " + e.getMessage());
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException("Substitute function failed on function " + functions[i].getName() + " " + e.getMessage());
            }
            try {
                FunctionColumnDescription cd = new FunctionColumnDescription(exp1.flatten(), functions[i].getName(), null, functions[i].getName(), false);
                odeSolverResultSet.addFunctionColumn(cd);
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
            }
        }
    }
    if (getSensitivityParameter() != null) {
        try {
            if (odeSolverResultSet.findColumn(getSensitivityParameter().getName()) == -1) {
                FunctionColumnDescription fcd = new FunctionColumnDescription(new Expression(getSensitivityParameter().getConstantValue()), getSensitivityParameter().getName(), null, getSensitivityParameter().getName(), false);
                odeSolverResultSet.addFunctionColumn(fcd);
            }
            Variable[] variables = simSymbolTable.getVariables();
            StateVariable[] stateVars = createStateVariables();
            for (int i = 0; i < variables.length; i++) {
                if (variables[i] instanceof Function && SimulationSymbolTable.isFunctionSaved((Function) variables[i])) {
                    Function depSensFunction = (Function) variables[i];
                    Expression depSensFnExpr = new Expression(depSensFunction.getExpression());
                    depSensFnExpr = simSymbolTable.substituteFunctions(depSensFnExpr);
                    depSensFnExpr = getFunctionSensitivity(depSensFnExpr, getSensitivityParameter(), stateVars);
                    // depSensFnExpr = depSensFnExpr.flatten(); 	// already bound and flattened in getFunctionSensitivity, no need here.....
                    String depSensFnName = new String("sens_" + depSensFunction.getName() + "_wrt_" + getSensitivityParameter().getName());
                    if (depSensFunction != null) {
                        FunctionColumnDescription cd = new FunctionColumnDescription(depSensFnExpr.flatten(), depSensFnName, getSensitivityParameter().getName(), depSensFnName, false);
                        odeSolverResultSet.addFunctionColumn(cd);
                    }
                }
            }
        } catch (MathException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error adding function to resultSet: " + e.getMessage());
        } catch (ExpressionException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error adding function to resultSet: " + e.getMessage());
        }
    }
    return odeSolverResultSet;
}

Example 9 with SimulationSymbolTable

use of cbit.vcell.solver.SimulationSymbolTable in project vcell by virtualcell.

the class SundialsSolver method getSensitivityParameter.

/**
 * Insert the method's description here.
 * Creation date: (6/27/2001 12:22:10 PM)
 * @return int
 */
public Constant getSensitivityParameter() {
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    Constant origSensParam = simSymbolTable.getSimulation().getSolverTaskDescription().getSensitivityParameter();
    // 
    if (origSensParam != null) {
        return (Constant) simSymbolTable.getVariable(origSensParam.getName());
    } else {
        return null;
    }
}

Example 10 with SimulationSymbolTable

use of cbit.vcell.solver.SimulationSymbolTable in project vcell by virtualcell.

the class SundialsSolver method createStateVariables.

/*
	This method was created in Visual Age
*/
private StateVariable[] createStateVariables() throws MathException, ExpressionException {
    Vector<StateVariable> stateVariables = new Vector<StateVariable>();
    // get Ode's from MathDescription and create ODEStateVariables
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    MathDescription mathDescription = simSymbolTable.getSimulation().getMathDescription();
    Enumeration<Equation> enum1 = ((SubDomain) mathDescription.getSubDomains().nextElement()).getEquations();
    while (enum1.hasMoreElements()) {
        Equation equation = (Equation) enum1.nextElement();
        if (equation instanceof OdeEquation) {
            stateVariables.addElement(new ODEStateVariable((OdeEquation) equation, simSymbolTable));
        } else {
            throw new MathException("encountered non-ode equation, unsupported");
        }
    }
    // Get sensitivity variables
    Variable[] variables = simSymbolTable.getVariables();
    Vector<SensVariable> sensVariables = new Vector<SensVariable>();
    if (getSensitivityParameter() != null) {
        for (int i = 0; i < variables.length; i++) {
            if (variables[i] instanceof VolVariable) {
                VolVariable volVariable = (VolVariable) variables[i];
                SensVariable sv = new SensVariable(volVariable, getSensitivityParameter());
                sensVariables.addElement(sv);
            }
        }
    }
    if (rateSensitivity == null) {
        rateSensitivity = new RateSensitivity(mathDescription, mathDescription.getSubDomains().nextElement());
    }
    if (jacobian == null) {
        jacobian = new Jacobian(mathDescription, mathDescription.getSubDomains().nextElement());
    }
    for (int v = 0; v < sensVariables.size(); v++) {
        stateVariables.addElement(new SensStateVariable((SensVariable) sensVariables.elementAt(v), rateSensitivity, jacobian, sensVariables, simSymbolTable));
    }
    if (stateVariables.size() == 0) {
        throw new MathException("there are no equations defined");
    }
    StateVariable[] stateVars = (StateVariable[]) BeanUtils.getArray(stateVariables, StateVariable.class);
    return (stateVars);
}